
@article{Ahmed,
  author = {Fahian Ahmed and Saddam Quirem and Gak Min and Byeong Kil Lee},
  title = {Hotspot Analysis Based Partial CUDA Acceleration of {HMMER 3.0} on {GPGPUs}},
  journal = {International Journal of Soft Computing and Engineering},
  isbn = {ISSN: 2231-2307},
  volume = {2},
  number = {4},
  month = {September},
  year = {2012},
  pages = {91--95}
}

%@inproceedings{DBLP:conf/cf/AjiFBN08,
@inproceedings{Aji,
  author    = {Ashwin M. Aji and
               Wu-chun Feng and
               Filip Blagojevic and
               Dimitrios S. Nikolopoulos},
  title     = {Cell-{S}Wat: modeling and scheduling wavefront computations
               on the cell broadband engine},
  booktitle = {Conf. Computing Frontiers},
  year      = {2008},
  pages     = {13-22},
  ee        = {http://doi.acm.org/10.1145/1366230.1366235},
  crossref  = {DBLP:conf/cf/2008},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

%@article{DBLP:journals/cluster/AkogluS09,
@article{Akoglu,
  author    = {Ali Akoglu and
               Gregory M. Striemer},
  title     = {Scalable and highly parallel implementation of Smith-Waterman
               on graphics processing unit using CUDA},
  journal   = {Cluster Computing},
  volume    = {12},
  number    = {3},
  year      = {2009},
  pages     = {341-352},
  ee        = {http://dx.doi.org/10.1007/s10586-009-0089-8},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{Altschul,
  title = {Basic local alignment search tool},
  author = {Stephen F. Altschul and Warren Gish and Webb Miller and Eugene W. Myers and David J. Lipman},
  journal = {Journal of molecular biology},
  volume = {215},
  number = {3},
  pages = {403--410},
  year = {1990},
  doi = {http://dx.doi.org/10.1016/S0022-2836(05)80360-2},
  publisher = {Elsevier},
  url = {http://www.sciencedirect.com/science/article/pii/S0022283605803602},
  abstract = {A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of \{MSP\} scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward \{DNA\} and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long \{DNA\} sequences. In addition to its flexibility and tractability to mathematical analysis, \{BLAST\} is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.}
}

@online{ArrayFire,
  title = {Comprehensive GPU function library},
  author = {AccelerEyes},
  year = {2014},
  howpublished = {Website},
  urldate = {April 2014},
  Url = {http://www.accelereyes.com/}
}

@online{Kronos,
  title = {KRONOS 840S Desktop Workstation},
  author = {CIARA Technologies Inc.},
  year = {2013},
  howpublished = {Website},
  Url = {http://www.ciaratech.com/product.php?id_prod=489&lang=en&id_cat1=1&id_cat2=9&id_cat3=129}
}

@book{cook,
  title={CUDA programming: a developer's guide to parallel computing with GPUs},
  author={Shane Cook},
  year={2013},
  publisher={Newnes}
}

@book{BioMach,
  title={Bioinformatics: the machine learning approach},
  author={Pierre Baldi and S{\o}ren Brunak},
  year={2001},
  edition = {2nd},
  publisher={MIT press}
}

@inproceedings{Derrien,
  title={Parallelizing HMMER for Hardware Acceleration on FPGAs},
  author={Steven Derrien and Patrice Quinton},
  booktitle={ASAP},
  pages={10--17},
  year={2007}
}

@book{SeqData,
  title={Sequence data mining},
  author={Guozhu Dong and Jian Pei},
  volume={33},
  year={2007},
  publisher={Springer Science+Business Media, LLC}
}

@inproceedings{Du,
  title={A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA},
  author={Zhihui Du and Zhaoming Yin and David A. Bader},
  booktitle={Parallel \& Distributed Processing, Workshops and Phd Forum (IPDPSW), 2010 IEEE International Symposium on},
  pages={1--8},
  year={2010},
  organization={IEEE}
}

@book{BioSeq,
  title={Biological sequence analysis: probabilistic models of proteins and nucleic acids},
  author={Richard Durbin},
  year={1998},
  publisher={Cambridge university press}
}

@article{HMMER3,
  title={Accelerated profile HMM searches},
  author={Sean R. Eddy},
  journal={PLoS computational biology},
  volume={7},
  number={10},
  pages={e1002195},
  year={2011},
  publisher={Public Library of Science}
}

@book{ProteinBio,
  title={Protein Bioinformatics: An algorithmic approach to sequence and structure analysis},
  author={Ingvar Eidhammer and Inge Jonassen and Willie R. Taylor},
  year={2004},
  publisher={J. Wiley \& Sons}
}

%@article{DBLP:journals/bioinformatics/Farrar07,
@article{SW-SSE2,
  author    = {Michael Farrar},
  title     = {Striped Smith-Waterman speeds database searches six times
               over other SIMD implementations},
  journal   = {Bioinformatics},
  volume    = {23},
  number    = {2},
  year      = {2007},
  pages     = {156-161},
  ee        = {http://dx.doi.org/10.1093/bioinformatics/btl582},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

%@inproceedings{DBLP:conf/bcb/GanesanCBT10,
@inproceedings{Ganesan,
  author    = {Narayan Ganesan and
               Roger D. Chamberlain and
               Jeremy Buhler and
               Michela Taufer},
  title     = {Accelerating HMMER on GPUs by implementing hybrid data and
               task parallelism},
  booktitle = {BCB},
  year      = {2010},
  pages     = {418-421},
  ee        = {http://doi.acm.org/10.1145/1854776.1854844},
  crossref  = {DBLP:conf/bcb/2010},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

%@article{Gotoh1982705,
@article{Gotoh, 
  title = {An improved algorithm for matching biological sequences},
  journal = {Journal of molecular biology},
  volume = {162},
  number = {3},
  pages = {705--708},
  year = {1982},
  issn = {0022-2836},
  doi = {http://dx.doi.org/10.1016/0022-2836(82)90398-9},
  url = [http://www.sciencedirect.com/science/article/pii/0022283682903989],
  author = {Osamu Gotoh},
  abstract = {The algorithm of Waterman et al. (1976) for matching biological sequences was modified under some limitations to be accomplished in essentially \{MN\} steps, instead of the \{M2N\} steps necessary in the original algorithm. The limitations do not seriously reduce the generality of the original method, and the present method is available for most practical uses. The algorithm can be executed on a small computer with a limited capacity of core memory. }
}

@article{DicBioinfo,
  title={Dictionary of bioinformatics and computational biology},
  author={John M? Hancock and Marketa J.Zvelebil},
  year={2004},
  publisher={John Wiley \& Sons}
}

@article{Henikoff,
  title={Amino acid substitution matrices from protein blocks},
  author={Steven Henikoff and Jorja G. Henikoff},
  journal={Proceedings of the National Academy of Sciences},
  volume={89},
  number={22},
  pages={10915--10919},
  year={1992},
  publisher={National Acad Sciences}
}

@online{Hsource,
  title = {HMMER source code release archives},
  author = {Howard Hughes~Medical Institute},
  year = {2014},
  howpublished = {Website},
  Url = {http://hmmer.janelia.org/software/archive}
}

@online{HMMER,
  title = {HMMER},
  author = {Howard Hughes~Medical Institute},
  year = {2014},
  howpublished = {Website},
  Url = {http://hmmer.janelia.org/}
}

@online{HMMER2,
  title = {HMMER2.3.2 source code release},
  author = {Howard Hughes~Medical Institute},
  year = {2014},
  howpublished = {Website},
  Url = {http://selab.janelia.org/software/hmmer/2.3.2/hmmer-2.3.2.tar.gz}
}

%@inproceedings{DBLP:conf/sc/HornHH05,
@inproceedings{ClawHMMER,
  author    = {Daniel Reiter Horn and
               Mike Houston and
               Pat Hanrahan},
  title     = {ClawHMMER: A Streaming HMMer-Search Implementation},
  booktitle = {SC},
  year      = {2005},
  pages     = {11},
  ee        = {http://doi.acm.org/10.1145/1105760.1105776},
  crossref  = {DBLP:conf/sc/2005},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@online{Intel,
  title = {Intel VTune Amplifier XE 2013},
  author = {Intel},
  year = {2014},
  howpublished = {Website},
  Url = {https://software.intel.com/en-us/intel-vtune-amplifier-xe/}
}

%@inproceedings{DBLP:conf/ipps/JacobLBC07,
@inproceedings{Jacob,
  author    = {Arpith C. Jacob and
               Joseph M. Lancaster and
               Jeremy D. Buhler and
               Roger D. Chamberlain},
  title     = {Preliminary results in accelerating profile HMM search on
               FPGAs},
  booktitle = {IPDPS},
  year      = {2007},
  pages     = {1-8},
  ee        = {http://dx.doi.org/10.1109/IPDPS.2007.370447},
  crossref  = {DBLP:conf/ipps/2007},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@mastersthesis{Kentie,
  title = {Biological {S}equence {A}lignment {U}sing {G}raphics {P}rocessing {U}nits},
  year = {2010},
  author = {M.A. Kentie},
  school = {Delft University of Technology},
  type = {Master Thesis}
}

%@book{Kirk:2010:PMP:1841511,
@book{Kirk,
  author = {Kirk, David B. and Hwu, Wen-mei W.},
  title = {Programming Massively Parallel Processors: A Hands-on Approach},
  year = {2010},
  isbn = {0123814723, 9780123814722},
  edition = {1st},
  publisher = {Morgan Kaufmann Publishers Inc.},
  address = {San Francisco, CA, USA},
}

%@article{Krogh19941501,
@article{Krogh,
  title = {Hidden Markov models in computational biology: Applications to protein modeling},
  journal = {Journal of molecular biology},
  volume = {235},
  number = {5},
  pages = {1501-1531},
  year = {1994},
  publisher = {Elsevier}
  issn = {0022-2836},
  doi = {http://dx.doi.org/10.1006/jmbi.1994.1104},
  url = {http://www.sciencedirect.com/science/article/pii/S0022283684711041},
  author = {Anders Krogh and Michael Brown and I. Saira Mian and Kimmen Sj{\"o}lander and David Haussler},
  abstract = {Hidden Markov Models (HMMs) are applied to the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated on the globin family, the protein kinase catalytic domain, and the EF-hand calcium binding motif. In each case the parameters of an \{HMM\} are estimated from a training set of unaligned sequences. After the \{HMM\} is built, it is used to obtain a multiple alignment of all the training sequences. It is also used to search the SWISS-PROT 22 database for other sequences that are members of the given protein family, or contain the given domain. The \{HMM\} produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate three-dimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a database fit the globin, kinase and EF-hand HMMs), the \{HMM\} is able to distinguish members of these families from non-members with a high degree of accuracy. Both the \{HMM\} and \{PROFILESEARCH\} (a technique used to search for relationships between a protein sequence and multiply aligned sequences) perform better in these tests than \{PROSITE\} (a dictionary of sites and patterns in proteins). The \{HMM\} appears to have a slight advantage over \{PROFILESEARCH\} in terms of lower rates of false negatives and false positives, even though the \{HMM\} is trained using only unaligned sequences, whereas \{PROFILESEARCH\} requires aligned training sequences. Our results suggest the presence of an EF-hand calcium binding motif in a highly conserved and evolutionary preserved putative intracellular region of 155 residues in the Œ±-1 subunit of L-type calcium channels which play an important role in excitation-contraction coupling. This region has been suggested to contain the functional domains that are typical or essential for all L-type calcium channels regardless of whether they couple to ryanodine receptors, conduct ions or both. }
}

%@inproceedings{DBLP:conf/aina/LandmanRW06,
@inproceedings{Landman,
  author    = {Joseph I. Landman and
               Joydeep Ray and
               John Paul Walters},
  title     = {Accelerating HMMer searches on Opteron processors with minimally
               invasive recoding},
  booktitle = {AINA (2)},
  year      = {2006},
  pages     = {628-636},
  ee        = {http://doi.ieeecomputersociety.org/10.1109/AINA.2006.67},
  crossref  = {DBLP:conf/aina/2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@book{IntroBio,
  title={Introduction to bioinformatics},
  author={Arthur M. Lesk},
  edition = {3rd},
  year={2013},
  publisher={Oxford University Press}
}

%@inproceedings{DBLP:conf/ipps/LigowskiR09,
@inproceedings{Ligowski,
  author    = {Lukasz Ligowski and
               Witold R. Rudnicki},
  title     = {An efficient implementation of Smith Waterman algorithm
               on GPU using CUDA, for massively parallel scanning of sequence
               databases},
  booktitle = {IPDPS},
  year      = {2009},
  pages     = {1-8},
  ee        = {http://dx.doi.org/10.1109/IPDPS.2009.5160931},
  crossref  = {DBLP:conf/ipps/2009},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{SW++,
  year={2009},
  journal={BMC Research Notes},
  eid={73},
  volume={2},
  number={1},doi={10.1186/1756-0500-2-73},
  title={{CUDASW++}: optimizing {S}mith-{W}aterman sequence database searches for {CUDA}-enabled graphics processing units},
  url={http://dx.doi.org/10.1186/1756-0500-2-73},
  publisher={BioMed Central},
  author={Liu, Yongchao and Maskell, DouglasL and Schmidt, Bertil},
  language={English}
}

@article{SW++2,
  year={2010},
  journal={BMC Research Notes},
  eid={93},
  volume={3},
  number={1},
  doi={10.1186/1756-0500-3-93},
  title={{CUDASW++2.0}: enhanced {S}mith-{W}aterman protein database search on {CUDA}-enabled {GPUs} based on {SIMT} and virtualized {SIMD} abstractions},
  url={http://dx.doi.org/10.1186/1756-0500-3-93},
  publisher={BioMed Central},
  author={Liu, Yongchao and Schmidt, Bertil and Maskell, DouglasL},
  language={English}
}


%@article{DBLP:journals/bmcbi/LiuWS13,
@article{SW++3,
  author    = {Yongchao Liu and
               Adrianto Wirawan and
               Bertil Schmidt},
  title     = {{CUDASW++ 3.0}: accelerating {S}mith-{W}aterman protein database
               search by coupling {CPU} and {GPU} {SIMD} instructions},
  journal   = {BMC Bioinformatics},
  volume    = {14},
  year      = {2013},
  pages     = {117},
  ee        = {http://dx.doi.org/10.1186/1471-2105-14-117},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@book{Loewy,
  author={Ariel G. Loewy, Philip Siekevitz, John R. Menninger and Jonathan A. N. Gallant},
  title={Cell Structure \& Function : An Integrated Approach},
  publisher={Saunders College Publishing},
  edition={3rd},
  year={1991}
}

%@inproceedings{DBLP:conf/reconfig/IsaBC12,
@inproceedings{FPGA,
  author    = {Mohd Nazrin Md. Isa and
               Khaled Benkrid and
               Thomas Clayton},
  title     = {A novel efficient {FPGA} architecture for {HMMER} acceleration},
  booktitle = {ReConFig},
  year      = {2012},
  pages     = {1-6},
  ee        = {http://dx.doi.org/10.1109/ReConFig.2012.6416723},
  crossref  = {DBLP:conf/reconfig/2012},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@mastersthesis{Maddimsetty,
  title = {Acceleration of Profile-{HMM} Search for Protein Sequences in Reconfigurable Hardware},
  year = {2006},
  author = {Rahul Pratap Maddimsetty},
  school = {Washington University in St. Louis},
  type = {Master Thesis}
}

@online{MAGMA,
  title = {A collection of next generation linear algebra (LA) GPU accelerated libraries MAGMA},
  author = {The University of Tennesse},
  year = {2014},
  howpublished = {Website},
  Url = {http://icl.cs.utk.edu/magma/software/}
}

%@article{manavski2008cuda,
@article{manavski,
  title={CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment},
  author={Manavski, Svetlin A and Valle, Giorgio},
  journal={BMC bioinformatics},
  volume={9},
  number={Suppl 2},
  pages={S10},
  year={2008},
  publisher={BioMed Central Ltd}
}

@book{Seq,
  title={Sequence Analysis in a Nutshell: A Guide to Tools: A Guide to Common Tools and Databases},
  author={Markel, Scott and Le{\'o}n, Darryl},
  year={2003},
  publisher={"O'Reilly Media, Inc."}
}

@online{Shader,
  title = {Compute shader overview},
  author = {Microsoft},
  year = {2014},
  howpublished = {Website},
  Url = {http://msdn.microsoft.com/en-us/library/windows/desktop/ff476331%28v=vs.85%29.aspx}
}

@online{HLSL,
  title = {Programming guide for \uppercase{HLSL}},
  author = {Microsoft},
  year = {2013},
  howpublished = {Website},
  Url = {http://msdn.microsoft.com/en-us/library/windows/desktop/bb509635%28v=vs.85%29.aspx}
}

@online{NCBI,
  title = {{NCBI} {NR}  (non-redundant) Protein Database},
  author = {National Center for Biotechnology Information},
  year = {2014},
  howpublished = {Website},
  urldate{7th April 2014},
  Url = {ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz}
}

%@article{Needleman1970443,
@article{Needleman,
  title = {A general method applicable to the search for similarities in the amino acid sequence of two proteins},
  journal = {Journal of molecular biology},
  volume = {48},
  number = {3},
  pages = {443-453},
  year = {1970},
  issn = {0022-2836},
  doi = {http://dx.doi.org/10.1016/0022-2836(70)90057-4},
  url = [http://www.sciencedirect.com/science/article/pii/0022283670900574],
  author = {Saul B. Needleman and Christian D. Wunsch],
  abstract = "A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to trace their possible evolutionary development. The maximum match is a number dependent upon the similarity of the sequences. One of its definitions is the largest number of amino acids of one protein that can be matched with those of a second protein allowing for all possible interruptions in either of the sequences. While the interruptions give rise to a very large number of comparisons, the method efficiently excludes from consideration those comparisons that cannot contribute to the maximum match. Comparisons are made from the smallest unit of significance, a pair of amino acids, one from each protein. All possible pairs are represented by a two-dimensional array, and all possible comparisons are represented by pathways through the array. For this maximum match only certain of the possible pathways must be evaluated. A numerical value, one in this case, is assigned to every cell in the array representing like amino acids. The maximum match is the largest number that would result from summing the cell values of every pathway. "
}

@online{CUDA-C,
  title = {{CUDA} C PROGRAMMING GUIDE},
  author = {NVIDIA},
  year = {2013},
  howpublished = {Website},
  Url = {http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html}
}

@online{CUDABest,
  title = {{CUDA} C Best Practices Guide},
  author = {NVIDIA},
  year = {2013},
  howpublished = {Website},
  Url = {http://docs.nvidia.com/cuda/cuda-c-best-practices-guide/index.html}
}

@online{Kepler,
  title = {Kepler Tuning Guide},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {http://docs.nvidia.com/cuda/kepler-tuning-guide/index.html}
}

@online{DirectCompute,
  title = {Directcompute {NVIDIA} developer zone},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {https://developer.nvidia.com/directcompute}
}

@online{CUDAzone,
  title = {{NVIDIA} CUDA zone},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {https://developer.nvidia.com/cuda-zone}
}

@online{CUDAwhat,
  title = {{NVIDIA} What is {CUDA}?},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {https://http://www.nvidia.com/object/cuda_home_new.html}
}

@online{Profiler,
  title = {Profiler User's Guide},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {http://docs.nvidia.com/cuda/profiler-users-guide/}
}

@online{CUDAlibs,
  title = {GPU-accelerated libraries},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {https://developer.nvidia.com/gpu-accelerated-libraries}
}

@online{cuBLAS,
  title = {CUDA Basic Linear Algebra Subroutines (cuBLAS) library},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {https://developer.nvidia.com/cublas}
}

@online{thrust,
  title = {A powerful library of parallel algorithms and data structures},
  author = {NVIDIA},
  year = {2014},
  howpublished = {Website},
  Url = {https://developer.nvidia.com/thrust}
}

%@inproceedings{DBLP:conf/ipps/OliverYS07,
@inproceedings{Oliver,
  author    = {Timothy F. Oliver and
               Leow Yuan Yeow and
               Bertil Schmidt},
  title     = {High Performance Database Searching with HMMer on FPGAs},
  booktitle = {IPDPS},
  year      = {2007},
  pages     = {1-7},
  ee        = {http://dx.doi.org/10.1109/IPDPS.2007.370448},
  crossref  = {DBLP:conf/ipps/2007},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@online{OpenCL,
  title = {The open standard for parallel programming of heterogeneous systems},
  author = {Khronos Group},
  year = {2014},
  howpublished = {Website},
  Url = {https://www.khronos.org/opencl/}
}

@online{cpus,
  title = {CPU Benchmarks},
  author = {PassMark Software},
  year = {2014},
  howpublished = {Website},
  Url = {http://www.cpubenchmark.net/high_end_cpus.html}
}

@book{BioFunc,
  title = {Bioinformatics and Functional Genomics},
  publisher = {John Wiley \& Sons},
  year = {2009},
  author = {Jonathan Pevsner},
  address = {New Jersey, USA},
  edition = {2nd}
}

@online{Pfam,
  title = {Wellcome Trust Sanger Institute and Howard Hughes Janelia Farm Research Campus},
  author = {Pfam database},
  year = {2013},
  howpublished = {Website},
  Url = {ftp://ftp.sanger.ac.uk/pub/databases/Pfam/releases/Pfam27.0/Pfam-A.hmm.gz}
}

%@inproceedings{DBLP:conf/ipccc/QuiremAL11,
@inproceedings{Quirem,
  author    = {Saddam Quirem and
               Fahian Ahmed and
               Byeong Kil Lee},
  title     = {CUDA acceleration of P7Viterbi algorithm in HMMER 3.0},
  booktitle = {IPCCC},
  year      = {2011},
  pages     = {1-2},
  ee        = {http://doi.ieeecomputersociety.org/10.1109/PCCC.2011.6108104},
  crossref  = {DBLP:conf/ipccc/2011},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

%@article{DBLP:journals/bioinformatics/RognesS00,
@article{SW-SIMD,
  author    = {Torbj{\o}rn Rognes and
               Erling Seeberg},
  title     = {Six-fold speed-up of {S}mith-{W}aterman sequence database searches
               using parallel processing on common microprocessors},
  journal   = {Bioinformatics},
  volume    = {16},
  number    = {8},
  year      = {2000},
  pages     = {699-706},
  ee        = {http://dx.doi.org/10.1093/bioinformatics/16.8.699},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{Rognes,
  title={Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation},
  author={Rognes, Torbj{\o}rn},
  journal={BMC bioinformatics},
  volume={12},
  number={1},
  pages={221},
  year={2011},
  publisher={BioMed Central Ltd}
}

%@article{DBLP:journals/pc/SachdevaKST08,
@article{Sachdeva,
  author    = {Vipin Sachdeva and
               Michael Kistler and
               Evan Speight and
               Tzy-Hwa Kathy Tzeng},
  title     = {Exploring the viability of the Cell Broadband Engine for
               bioinformatics applications},
  journal   = {Parallel Computing},
  volume    = {34},
  number    = {11},
  year      = {2008},
  pages     = {616-626},
  ee        = {http://dx.doi.org/10.1016/j.parco.2008.04.001},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@article{Saeed,
  title={Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors},
  author={Ali Khajeh Saeed and Stephen Poole and J. Blair Perot},
  journal={Journal of Computational Physics},
  volume={229},
  number={11},
  pages={4247--4258},
  year={2010},
  publisher={Elsevier}
}

%@book{Sanders:2010:CEI:1891996,
@book{CUDAintro,
  author = {Sanders, Jason and Kandrot, Edward},
  title = {{CUDA} by Example: An Introduction to General-Purpose {GPU} Programming},
  year = {2010},
  isbn = {0131387685, 9780131387683},
  edition = {1st},
  publisher = {Addison-Wesley Professional},
}

%@article{smith1981identification,
@article{SW,
  title={Identification of common molecular subsequences},
  author={Smith, Temple F and Waterman, Michael S},
  journal={Journal of molecular biology},
  volume={147},
  number={1},
  pages={195-197},
  year={1981},
  publisher={Elsevier}
}

@online{Swiss-Prot,
  title = {UniProtKB/Swiss-Prot protein knowledgebase release 2014-05 statistics},
  author = {SIB Bioinformatics Resource Portal},
  year = {2014},
  howpublished = {Website},
  Url = {http://web.expasy.org/docs/relnotes/relstat.html}
}

@online{UniProtTr,
  title = {UniProtKB/TrEMBL PROTEIN DATABASE RELEASE 2014\_05 STATISTICS},
  author = {EMBL-EBI, Wellcome Trust Genome Campus},
  year = {2014},
  howpublished = {Website},
  Url = {http://web.expasy.org/docs/relnotes/relstat.html}
}

@online{UniProt,
  title = {UniProt Release},
  author = {Universal Protein Resource},
  year = {2014},
  howpublished = {Website},
  Url = {ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2013_09/}
}

@online{upr,
  title = {About UniProtUniversal Protein Resource},
  author = {Universal Protein Resource},
  year = {2014},
  howpublished = {Website},
  Url = {http://www.uniprot.org/help/about}
}

%@inproceedings{DBLP:conf/aina/WaltersQC06,
@inproceedings{Walters2006,
  author    = {John Paul Walters and
               Bashar Qudah and
               Vipin Chaudhary},
  title     = {Accelerating the HMMER Sequence Analysis Suite Using Conventional
               Processors},
  booktitle = {AINA (1)},
  year      = {2006},
  pages     = {289-294},
  ee        = {http://doi.ieeecomputersociety.org/10.1109/AINA.2006.68},
  crossref  = {DBLP:conf/aina/2006},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

%@inproceedings{DBLP:conf/ipps/WaltersBKC09,
@inproceedings{GPUHMM,
  author    = {John Paul Walters and
               Vidyananth Balu and
               Suryaprakash Kompalli and
               Vipin Chaudhary},
  title     = {Evaluating the use of GPUs in liver image segmentation and
               HMMER database searches},
  booktitle = {IPDPS},
  year      = {2009},
  pages     = {1-12},
  ee        = {http://dx.doi.org/10.1109/IPDPS.2009.5161073},
  crossref  = {DBLP:conf/ipps/2009},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@online{Waters,
  title = {Taking CUDA to Ludicrous Speed},
  author = {Blue Waters},
  year = {2013},
  howpublished = {Website},
  Url = {http://iclcs.uiuc.edu/index.php/iclcs-news/51-blue-waters-undergraduate-petascale-internship-program.html}
}

@online{Cell,
  title = {Cell (biology)},
  author = {Wikipedia},
  year = {2014},
  howpublished = {Website},
  Url = {http://en.wikipedia.org/wiki/Cell_(biology)}
}

@online{sa,
  title = {Sequence Alignment},
  author = {Wikipedia},
  year = {2014},
  howpublished = {Website},
  Url = {http://en.wikipedia.org/wiki/Sequence_alignment}
}

@book{CUDAHand,
  title={The CUDA Handbook : A Comprehensive Guide to GPU Programming},
  author={Nicholas Wilt},
  year={2013},
  publisher={Addison-Wesley Professional},
  pages={528},
  isbn={978-0321809469}
}

%@inproceedings{DBLP:conf/IEEEpact/WunBC05,
@inproceedings{Wun,
  author    = {Ben Wun and
               Jeremy Buhler and
               Patrick Crowley},
  title     = {Exploiting Coarse-Grained Parallelism to Accelerate Protein
               Motif Finding with a Network Processor},
  booktitle = {IEEE PACT},
  year      = {2005},
  pages     = {173-184},
  ee        = {http://doi.ieeecomputersociety.org/10.1109/PACT.2005.21},
  crossref  = {DBLP:conf/IEEEpact/2005},
  bibsource = {DBLP, http://dblp.uni-trier.de}
}

@online{Zeller,
  title = {Tutorial CUDA},
  author = {Cyril Zeller},
  year = {2014},
  howpublished = {Website},
  Url = {http://people.cs.pitt.edu/~melhem/courses/3580p/nvidia.pdf}
}
